The Genome Conspiracy
by NicelyDoneOver
Summary: First FF offering so please be constructive. The human genome has been mapped and after being duped into participating, Sheldon finds himself and his friends in a project that dwarfs anything mankind has previously attempted - the survival of the human race. May get racy but for now strong T. Some Lenny, some MelRaj, OFC
1. Sampling and Subterfuge

The Genome Revelation

It was Howard's idea.

It was Halo night and, as usual, Sheldon was holding court about how his superior intellect almost ensured his team's victory. Penny just rolled her eyes and snarked, "Oops, plasma bomb. Sorry about that, sweetie!"

"Penny! Must I remind you that you are _my_ partner in this campaign?" He reemerged into play and hid behind some rubble in order to get his bearings and –

"Gotcha!" Sheldon's avatar's head exploded and Penny giggled. "Sorry, honey, just thought I'd remind you that 'superior intellect' alone doesn't ensure victory. It takes teamwork and planning and ruthless execution - " she grunted and glared at Howard after being killed by a poorly thrown grenade.

"Y'know, Sheldon, considering your family and all, I'm surprised you're as intellectually gifted as you are." It was a double-edged comment and knowing Sheldon, Howard rightly assumed he'd preen in what he perceived as flattery – and he did.

"Well, Howard – "

"All that intellect didn't save you from Penny," Raj piped up, a wine cooler in his hand.

"She's supposed to be my partner! And besides – " but Howard's musings cut him off but also got his attention.

"Guys, and Penny," he said, nodding to Penny who was most definitely not a guy by anyone's definition, "You can get your Personal Genomics Analysis for only $99 plus shipping. I'm thinking about doing it. If Bernie and I ever decided to have kids it would be worth it to know what traits we could expect our kids to have. And then there's the whole question about possible genetic predisposition to diseases."

Penny was intrigued by the idea. To know what the future held in store for her was something she craved. It's why she went to psychics and palm readers and read her horoscope every day. She wanted to know what her future held.

Sheldon thought having his genome analyzed and mapped was a wonderful idea. It would provide him with glimpses of his ancestry that his own family didn't seem too interested in knowing. His mother had been adopted and his father…the less said the better about any of _his_ forebears.

"I'm in. I find this to be a fascinating concept…having one's own past and future outlined on a few sheets of paper…something that will buttress my belief that I am Homo novus…the New Man. I'll devote an entire chapter in my memoirs to it."

"How much does it cost again?" asked Penny. Money was always an issue.

"If we all do it, I will pay for Penny's as well. I wish Leonard were here. He would definitely want to know about his and Penny's offspring…like how tall they would be and if they'd inherit a predispostion towards myopia and lactose intolerance."

Penny gave Sheldon a startled look and then turned away, teary-eyed. He could be an ass, sure, but other times, like this one, he was the most thoughtful man she'd ever met.

Howard handled all the details and 4 days later he showed up at the apartment with Bernie and 6 kits.

"Because we submitted a group application, shipping is free. All you have to do is read the directions, seal the samples and give me your kits and I'll have FedEx pick them up."

It was once again Halo Night and the four friends plus Bernadette were laughing and drinking and eating snacks and watching Penny and Sheldon slaughter their opponents. Howard interrupted the game to take a call on his cell but Penny kept on killing him as soon as he reemerged into the game. After a few sentences, Howard hung up his phone and turned off the game console and held up his hands.

"Quiet, please! That call was from Genomics Testing Service. They tried to deliver our results but I'm not home. Get this! They're coming over here to personally deliver our results! Man, that's some customer service."

Everyone started talking at once but Howard again motioned for quiet. "Listen, all the results are in but Sheldon's…something about a corrupted sampling error in their lab. Sheldon, they want to refund your money, obtain another test sample and…wait for it…they're going to do it for free, Sheldon. Free! And just to make sure you remain a satisfied customer, the courier delivering our results is supposed to wait until you provide them with the samples – and obtain a DNA swab – and they'll provide an entire DNA analysis…for free!"

Sheldon was initially disappointed and of course mentally preparing a stern letter decrying sloppy laboratory procedures when the 'refund your money' registered. When he replayed Howard's prattling in his mind, he became very excited.

"Oh, free? And they'll redo the entire process _and_ throw in DNA Analysis as well? All free?"

"Yes, exactly. Free, as in, you get something without an exchange of specie'," Howard elaborated.

"Well, considering the magnitude of their error – " Sheldon's response was interrupted by a knock at the door. Raj opened the door and ushered in a courier from FexEx and an older gentleman wearing a white lab coat and carrying a shipping container.

"Which of you is Dr. Sheldon L. Cooper?" the man in the white lab coat asked.

"I am Dr. Sheldon L. Cooper." Sheldon stood and approached the older bearded man while the blonde girl from FedEx obtained signatures on an unusual number of forms and distributed packages to each of the others in the room.

The man looked Sheldon up and down and then put on latex surgical gloves. "May I see some identification, please? We at Genomics Testing are mortified by the lab error and it is my personal responsibility to squire these samples through the testing process and return the results as quickly as possible. At Genomics Testing, we pride ourselves on infallibility and this error has come as quite a shock to us."

"Yes, I'm sure it does. Mass production of such sensitive data is – " but the man interrupted Sheldon's diatribe and repeated, "May I see some identification, please?"

Sheldon hated being interrupted but he produced his CalTech ID. "As I was saying – " but the man interrupted Sheldon yet again and said, 'Please open your mouth so that I may obtain a swab of saliva for DNA sequencing and reporting." He held a swab in one hand and a strange test tube in the other.

"Well, I – urk!" The man jabbed the swab into Sheldon's open mouth and then inserted it into the test tube and sealed it. He turned to Sheldon with a glass container and thrust it at him. "Go. Produce a sample and I will be on my way. I shall perform the analysis and testing myself to ensure proper results. Go. The sooner I have the specimen the sooner I'll have my results."

Sheldon quickly returned and the man took the sample, holding it in both hands, and almost reverently placed it in the shipping container which contained foam cutouts for the test tube and the sample container.

"May I please have a photograph, Dr. Cooper? It is an honor and privilege to meet a man of your reputation. This will be placed in a place of honor in our lobby." Sheldon blushed but couldn't say no. The man played to his vanity and took several photos, front and both sides, 'to ensure we have the best photo available'.

He followed the FedEx rep out the door and down the stairs and got into a FedEx truck that was nothing like a regular FedEx truck on the inside. The entire cargo area was filled with banks of surveillance equipment, communications gear and monitors. A large African-American man said, "Well, did you get it?"

"Of course, Colonel Hatch. Has the sister been taken into custody yet?" He was busy peeling off his beard and mustache after placing the latex gloves he'd worn in a haz-mat container. When he was finished, he didn't look much older than Sheldon, especially after the gray hair coloring was washed out.

"_They_ said to wait until you had a second sample confirming the anomaly and the DNA sequencing. You know how _They_ are. He's not someone who can just 'disappear' if we're wrong – if _you're_ wrong."

The Colonel turned and sat down at one of the monitors that relayed images from one of the scores of bugs planted throughout the apartment. He watched as the group played a video game and discussed their genome reports, all except Sheldon, of course. He and the pretty blonde were busy destroying critters and their fellow players at Halo.

'_Strange,'_ the colonel mused to himself, _'he's not at all what I expected. Well, the Lord works in mysterious ways His wonders to perform. And this character just might save us all!'_

There are 3.3 _billion_ pairs of base-pairs in the human genome. Sheldon Cooper had 4_ billion _base-pairs_! _Considering the threat facing all of humanity, _They _believed that individuals possessing abnormal genomes just might be the next stage of human evolution and it was this belief that had spawned the S-S Project and the façade that was Genomics Testing Service. Of the tens of thousands of people who had submitted samples, only Sheldon Cooper was singled out for retesting.

Three Days Later

Applebee's

Galveston, Texas

"Hi, welcome to Applebee's! Two for lunch?" She eyed the short blonde woman and the tall African American man and wondered what the Air Force was doing eating lunch here. She had the oddest thought patterns.

"We need to speak with Melissa Cooper. Can you – "

"I'm – I'm Melissa Cooper. Can I help you with something? If you're recruiters, I'm really not interested." Life for her was all about having a good time, burning the candle at both ends. Her favorite aphorism was 'Live fast, die young, leave a good looking corpse' and being in the Air Force so wasn't her idea of a viable occupation.

"Miss Cooper, I need you to come with us. You're not in trouble but – your brother is. Please, we'll square things with your employer and even make up for lost wages. Your brother needs you, Miss Cooper."

"Shelly? In trouble? But he's a physicist – oh my God, did he build another atomic bomb or something because if he did, you really need to be talking to my Momma because – "

"_Miss Cooper, _shut up and come with us. It's imperative that you talk with your brother. It's a national security matter and we don't have much time. Please – if you love your country and your brother – come with us right now!" The short blonde spoke without moving her jaw and Melissa's unkind thought was 'one of them Yankee women with a stick up her ass'

"Let's go. Time's a-wasting!" Melissa was out the door before either of the two could react.

CalTech

Office of Dr. Sheldon L. Cooper

Pasadena, California

"Mom, I'm sure Melissa hasn't run off with anyone and been engaging in coital activities. She has better sense than that, doesn't she?" His mother had finally called after being told that she couldn't file a missing person's report for another 24 hours.

"She walked out of Applebee's at lunch time, Shelly, and that's the last anyone's seen of her. Her car's still in employee parking and it's been 24 hours – "

"Mom, what do you want?" He was blunt but not mean. He simply didn't have time for his mother's hysterics and he was not interested at all in what Jesus would do about the situation but she was still his mother and he loved her.

"Come home. Junior's out in the Gulf on some oilrig and out of touch and Mee Maw, well, I haven't told her that Melissa's gone missing. Please come home. It's your responsibility as the remaining available man in the family to come home and help me find Melissa. Oh, my! What if she's been kidnapped by human traffickers? Oh, Lord, Sheldon – "

"Mom, I'll arrange vacation and see you in a few days. I'll have to confirm the train – "

"You get your butt on an aeroplane, Sheldon Cooper, and right snappy. A train – Missy could be sold to some Middle Eastern potentate by the time you get here. Call me with flight arrival times and I'll meet you at the airport."

Colonel Hatch took off his headphones and laughed loudly. That boy's momma would drive any man to drink given enough exposure. He typed in a brief command and watched on a monitor as Sheldon took out a phone directory and started scanning the yellow pages. He didn't care what number Dr. Cooper dialed. It would be answered here.

"Moira, get your accent ready. Dr. Cooper is about to make a plane reservation."

The short blonde smiled and prepared to answer the call. "Manila or Mumbai, sir?"

"Texas."

"Hello, Southwest? I need to get on the next available flight to Galveston. I don't care what it costs and I'll stand up if necessary. Please…" Sheldon was desperate. He loved his sister despite his protestations and if something happened to her he didn't know what he'd do.

'He sounds desperate and so unlike the dickhead I met up at the apartment when I got his friends to sign non-disclosure agreements and the 'treason and sedition acknowledgement' forms. I almost feel sad for him. He thinks his sister is in danger when really, it's him.'

"Dr. Cooper, there are no seats available for flights until Thursday, I'm sorry. I checked all the airlines as a courtesy and it's impossible to get anywhere near Texas because of weather and flight cancellations. But - "

"Yes? But what?"

"Um, we do have a freight flight that is flying directly into Galveston. It's not subject to passenger safety regulations and we do have one seat on the flight leaving LAX in 3 hours. Do you want it? It's just a jump seat but it will get you to Galveston. We usually ferry pilots from deadheads."

"Give me the information on terminal location and – "

"We fly our cargo out of a private field, Dr. Cooper. I'll send a van for you if that's not too much of an imposition?"

Imposition? Was this woman crazy? It was like a miracle!

"That would be most convenient. You have my credit card information on file." He gave the woman his cell number and hung up. He had packing to do and only two hours to get ready to leave.


	2. A Skeptical Sheldon

King Khalid City  
Saudi Arabia  
3 Months Prior to the Events in Chapter One

Amelia Farrah Fowler re-read the email she had composed to Sheldon Cooper for the third time and finally sighed and pressed 'SEND'. She leaned back in the way-too-comfortable leather computer chair and pressed a tissue to her eyes. After more than three years of failing to find the key to triggering Sheldon's limbic system into life, she terminated the relationship agreement. That beautiful mind, those burning blue eyes and those adorable OCD quirks – _Oh, what am I going to do without you, Sheldon? I can't just be your 'friend who happens to be a girl'. I'm needy and greedy and I wanted it all and now I can have it –_

A change in air pressure alerted her that she was no longer alone in her palatial office. She dabbed her eyes just once more and then discarded the tissue just as she had the man she'd convinced herself she loved.

"Amy, it is time. Are you ready, my precious gem?" The tall man was impeccably dressed in a business suit and was looking at his watch and tapping its face.

She was wearing a simple white business suit with a green crepe blouse and the traditional headscarf. The massive engagement ring seemed to sparkle with light and she looked up at the tall man and gave him a watery smile. The die was cast.

"Yes, Faisal. Let's go meet my future mother-in-law."

* * *

Pasadena Municipal Airport  
Present Day

The van had appeared at his apartment precisely on time and the driver had spared Sheldon the necessity of listening to mindless drivel after confirming his identity and stowing his luggage in the rear. His mind was concentrating on Melissa. He could still feel their mysterious 'twin bond' so he knew she was still alive. Before he knew it, they were at their destination and the driver was holding open the van door after retrieving his luggage.

A man dressed in commercial pilot's garb greeted him and led him up stairs to a jet way that connected to the aircraft that was strangely dark unlike the other well-lit planes he could see on either side.

"Welcome aboard, Dr. Cooper. Stow your bag under that shelf and please secure the hatch. Now, we operate under more relaxed rules since we're hauling freight but we have some rather draconian crew rules to abide by. Please note that your seatbelt is similar to that used in military aircraft but also that wearing oxygen masks is obligatory for maximizing safety in un-pressurized aircraft."

The copilot strapped Sheldon in and then fitted the tight-fitting oxygen mask over his head and onto his face and secured it. He pointed to a red fitting on his own mask and Sheldon heard a muffled 'press this in order to access the intercom' and then the man disappeared forward and took his seat and prepared for takeoff.

"Is he strapped in and masked?" asked the pilot.

"Yes. Hit him with the gas and then get this bird in the air. Home Base wants us there in under an hour." He watched the pilot open a safety cover and press and hold a red button for a count of five and then release it and close the cover. "Tower, this is US Air Force flight 675 requesting priority takeoff – Over."

Sheldon thought the mask smelled strange but tabled that thought as he heard the engines begin to whine through start up and then…nothing.

* * *

Home Base  
Nevada

"Colonel Hatch, Dr. Cooper has been secured without mishap and ETA is 57 minutes." She tried to ignore the Colonel's black eye and broken nose. She fought to contain the smirk that threatened to break out every time she saw the colonel and was reminded of just how he got those injuries.

Moira Soames watched the monitors relaying images from Melissa Cooper's guest quarters as the young woman paced back and forth like a caged tiger. Once the situation had been explained to her and she'd been tested, Melissa had demanded that she be able to contact her family to let them know she was safe.

"Ms. Cooper, Melissa, I'm afraid that is impossible. Your body will be found just outside of town near a landfill in a few days, the victim of senseless violence. I'm sorry but it has to be this way because - "

Missy immediately attacked the colonel thinking that he was going to kill her and it took two of the security staff to restrain her from further maiming her 'kidnapper'. Moira had been brought in to explain the situation as best she could. Moira only escaped being maimed because of her advanced training in unarmed combat and the two security guards standing by.

When she finally calmed down enough to understand the situation more fully, she laughed out loud and said the last thing anyone heard her say: "Shelly's gonna tear this place apart when he finds out you've killed us both off for this project of yours. God help you all if Meemaw has a stroke of sumthin'. You have no idea who you be fuckin' with, little girl."

Moira just smiled. She did know. She knew more about Sheldon Lee Cooper than anyone on this planet outside of the man himself and maybe his beloved Meemaw. When his name appeared on the Project's 'Persons of Interest' list, she'd tasked the various intelligence services of the nations involved to develop an intelligence profile.

She now knew his schedules, his likes (few) and dislikes (numerous), his dalliance with a married woman in Germany as a mere teenager and specifically of his going-nowhere-now-dead relationship with Dr. Amelia Farrah Fowler. A few words whispered in the right ears and that particularly troublesome arrangement had become a thing of the past. She'd read Fowler's email and wondered how someone as incredibly intelligent as Dr. Cooper could have allowed himself to be manipulated by someone who was unable to accept him for who he was?

Her gaze fell on a mission clock that hung near her workstation. In fact, a similar clock was in every office, hallway and residential quarters throughout the complex.

3:7:24:11:27

She took a cleansing breath and went to greet the air freighter after it had been brought into the hangar. She looked at Colonel Hatch again and this time the smile flitted across her face before she could stop it. _Missy Cooper and I have a lot more in common than she knows. I'm about to become her best friend. What better source of additional insights into the renowned particle physicist than someone who has spent her entire life trying not to be just like him_

* * *

Home Base  
Dispensary  
Nevada

"He's not responding like he should. He had the standard dosage based on weight and body type and there's no reason he hasn't regained consciousness yet."

"Get his sister in here. Maybe a familiar voice will bring him out of it. Obviously Cooper is very susceptible to anesthesia, something that wasn't in his file."

Missy was brought into the dispensary and saw her brother lying on a gurney, all kinds of medical monitoring equipment hanging from racks and stands all around him.

Colonel Hatch explained the situation to her via CCTV. He wasn't going to risk his life again trying to reason with that Texas hellcat. Missy just glared at the medical staff and shook herself from the two security guards and walked quickly to her brother's side.

"He's a shallow breather. Get him up and on his feet and walk him around. He'll snap out of it in a few minutes. The same thing happened when he ruptured his appendix years ago. He doesn't handle anesthesia well at all."

Moira stood beside Missy and looked at Sheldon and sighed. Missy glanced over and raised an eyebrow and said, "You best lose the attitude if'n you want any cooperation at all from the Coopers. Shelly's different. He's always been different. Why should this be any different?"

"His cooperation is critical, Melissa, yes, but I'm just worried that we didn't know about this. Our studies and research – "

Missy stared at the girl for a moment and then laughed quietly. "Your left contact lens is slipping. Why bother with a disguise at this point? It's not like you're ever goin' to let us leave here alive."

Moira smiled and blushed. She pulled a contact case from her tunic pocket and removed the colored lenses and when she looked up and at Missy, the girl stepped back, alarmed.

Dark emerald-green eyes stared back at her. The irises were exactly like a cat's.

"What _are _you?"

* * *

Luckily for all involved, Sheldon's wheezy cough interrupted the confrontation and Missy rushed to his side, telling him everything was going to be all right and that now they would 'open up a can of whoop-ass and get the fuck outta here!'

Cooler heads prevailed albeit not at first. The two burly security guards stood on either side of Missy, each with hand on her shoulder to make sure she stayed seated. Sheldon sat quietly and listened to the explanation Colonel Hatch had laid out after Sheldon had dismissed Moira's attempts at maintaining proper protocol. He had simply ignored her and asked one of the technicians to 'be a lamb and fetch whomever is in charge here'.

Now Sheldon pinched the bridge of his nose and wished he had Raj Koothrappali with him to refute the preposterous claims and plans laid out before him but he didn't.

He sighed and stared at his sister who was also processing all that she'd heard for the first time when the battered colonel had made his case to her brother.

"Shelly, what do you think of all this?" Her voice was calm and betrayed none of the fear and anger she felt. He knew that she was 'ducking' at this very moment just as he was. 'Ducking' was the phrase his Meemaw used to explain how a body could be calm on the outside and 'in a considerable bother' inside, like a calm duck on a pond whose webbed feet were going a mile a minute.

"Yes, Dr. Cooper, what do you think?" Colonel Hatch was a bit put off by the tall, thin man sitting on the gurney, swinging his feet back and forth like a child.

"I think I would be more inclined to believe you if I had the confirmation of your wildly unlikely tale from someone I know and trust. And, I would pose a question to you. Why me, us, I mean?"

The colonel nodded and said, "Give us a name and we'll fetch him. As for 'why you'? Would you entrust the continuation of the species to lesser men and women?" The psych profile had suggested playing to his enormous ego and vanity and it appeared to be working.

"What about 'Cat Woman' over there? Is she one of your saviors?" said Missy to the colonel.

Moira blushed and looked down at her fists on her lap, clenched in anger and humiliation. This is exactly why she wore contact lenses. She should be used to it but it still hurt.

"Missy, hush your mouth. There's no reason to be rude and certainly not to strangers who could easily discard your body in a landfill somewhere with the rest of this facility's trash." He had unknowingly hit on the exact scenario that had resulted in the colonel's shiner and broken nose.

"Besides," he continued in a tone of voice suggesting that she should know better, "aren't you and I freaks? You chose to hide your abilities in exchange for social acceptance. You faked test results, played the dumb country girl and settled for far less than you could have had. People who live in glass houses, Missy…"

He looked over at the colonel and smiled a real smile, not the Jokeresque grimace that those who knew him from Pasadena often saw.

"Enlist Dr. Rajesh Koothrappali in this little cabal of yours. If he confirms your data and conclusions, then you will have my full cooperation and participation."

He stood up and swayed for a second but caught his balance and walked over to Moira Soames and took her balled fists in his hands.

"I apologize for my sister's unforgivable rudeness. I'm Dr. Sheldon Cooper and I think you look much more esthetically pleasing in your current attire than in your FedEx uniform."

Moira felt his warm hands on her fists and relaxed and smiled up at him and blurted out "I expected you to say 'I'm Batman'. I'm Moira Soames, Dr. Cooper."

The colonel cleared his throat and then suggested that she take the Coopers on a tour of the unclassified areas of the facility while he made arrangements for the arrival of Dr. Koothrappali.

* * *

Caltech Cafeteria

Raj and Howard were eating lunch in the cafeteria when Dr. Gabelhauser, accompanied by two large gentlemen in suits, asked Raj for a few moments in private.

Within minutes, Rajesh Koothrappali was in handcuffs and being shoved into an INS van after being told that his visa was being revoked and he was being deported. Despite Dr. Gabelhauser's assurances that he would have the mattered settled, Rajesh Koothrappali was never seen again.

* * *

Home Base  
Nevada

Raj blinked at the sudden light and glanced around and was relieved to see two familiar faces in the crowded cafeteria that was eerily similar to the one at CalTech.

"Sheldon! Missy! What ever is going on here?" Raj had been taken to the local airport, blindfolded and then handcuffed to a very uncomfortable airline seat and flown to Home Base and immediately escorted to the cafeteria where Sheldon and Missy were eating a late lunch.

"Hello, Raj, I'm so glad you got over that freaking 'selective mutism' of yours, honey. Sit down and let Cat Woman and Shelly lay it all out for you while I get you something to eat and drink." She fell back on her comfort zone. Feed a man and he was putty in your hands.

"Missy, you – Sheldon – _Cat Woman?_" He sat down heavily and muttered something in Hindi.

"Raj, Mother Kali is an appropriate deity to invoke, considering the circumstances of your unconventional invitation – " Sheldon would have gone on and on but Raj interrupted him, his voice bordering on hysterical.

"_Unconventional_? Sheldon, I was dragged from CalTech, thrown in an INS van with other poor souls and then dragged onto an aircraft, handcuffed and blindfolded and now – "

"Raj, I need your help with something that is so monumentally earth shattering that – oh, and this is Ms. Moira Soames, not Cat Woman. Have some sense of civility and propriety - "

Raj began to mutter in Hindi and Sheldon turned to Moira with an apologetic smile.

"He really _is_ the foremost man in his field despite his current state of mind. Please don't take offense at his comments. He's really quite brilliant when his mind is focused."

"Really, Sheldon? 'Quite brilliant'? Okay, who are you and what have you done with my friend?"

Missy returned with a Chef's salad and ice tea for Raj and said, "Raj, believe me, it's Shelly. No one can possibly be as insulting when delivering a compliment as my dear older brother."

"Sarcasm, Missy? Surely you know that…"

Moira tuned out the actual words and marveled at the dynamic between the two siblings and their Indian friend. She never would have guessed at the bond that existed between them and she felt a moment of jealousy but quashed it.

"Dr. Koothrappali, Dr. Cooper wants your opinion on some studies we've conducted. As an astrophysicist, he values your input and needs your opinion on something of grave importance to all of us."

Missy snickered. "Cat Woman wants you to tell Shelly if the end of the world is just around the corner, Raj."


End file.
